Hoang Tan Nguyen
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/CNVrd2 |
| git_branch: RELEASE_3_13 |
| git_last_commit: 0a3ceac |
| git_last_commit_date: 2021-05-19 12:01:50 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:01 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the CNVrd2 package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CNVrd2.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 354/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CNVrd2 1.30.0 (landing page) Hoang Tan Nguyen
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CNVrd2 |
| Version: 1.30.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNVrd2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CNVrd2_1.30.0.tar.gz |
| StartedAt: 2021-10-14 21:21:03 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 21:26:11 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 307.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CNVrd2.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CNVrd2.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings CNVrd2_1.30.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/CNVrd2.Rcheck'
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CNVrd2/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CNVrd2' version '1.30.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'CNVrd2' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
'DNAcopy' 'Rsamtools'
All declared Imports should be used.
Packages in Depends field not imported from:
'VariantAnnotation' 'ggplot2' 'gridExtra' 'methods' 'parallel'
'rjags'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
groupCNVs,clusteringCNVs: warning in matrix(0, nr = length(x2), ncol =
k - 2): partial argument match of 'nr' to 'nrow'
segmentSamples,CNVrd2: warning in matrix(0, nr = nnn, ncol =
dim(genes)[2]): partial argument match of 'nr' to 'nrow'
calculateLDSNPandCNV: no visible global function definition for
'TabixFile'
calculateLDSNPandCNV : readChunkVCF: no visible global function
definition for 'GRanges'
calculateLDSNPandCNV : readChunkVCF: no visible global function
definition for 'readVcf'
calculateLDSNPandCNV : readChunkVCF: no visible global function
definition for 'geno'
calculateLDSNPandCNV: no visible global function definition for
'mclapply'
calculateLDSNPandCNV : calcPandR2 : LDandP: no visible global function
definition for 'fisher.test'
calculateLDSNPandCNV : calcPandR2 : LDandP: no visible global function
definition for 'chisq.test'
calculateLDSNPandCNV : calcPandR2: no visible global function
definition for 'p.adjust'
groupBayesianCNVs: no visible global function definition for
'jags.model'
groupBayesianCNVs: no visible global function definition for 'update'
groupBayesianCNVs: no visible global function definition for
'coda.samples'
groupBayesianCNVs: no visible global function definition for 'dnorm'
groupBayesianCNVs: no visible global function definition for 'par'
groupBayesianCNVs: no visible global function definition for 'hist'
countReadInWindow,CNVrd2: no visible global function definition for
'readDNAStringSet'
countReadInWindow,CNVrd2 : countReadForBamFile: no visible global
function definition for 'write.table'
countReadInWindow,CNVrd2: no visible binding for global variable
'objectCNVrd2'
countReadInWindow,CNVrd2: no visible global function definition for
'ScanBamParam'
countReadInWindow,CNVrd2 : <anonymous>: no visible global function
definition for 'countBam'
countReadInWindow,CNVrd2 : gcContent: no visible global function
definition for 'unmasked'
countReadInWindow,CNVrd2 : gcContent: no visible binding for global
variable 'Hsapiens'
countReadInWindow,CNVrd2 : gcContent: no visible global function
definition for 'alphabetFrequency'
emnormalCNV,clusteringCNVs : loglk : <anonymous>: no visible global
function definition for 'dnorm'
emnormalCNV,clusteringCNVs : initialValues: no visible global function
definition for 'kmeans'
emnormalCNV,clusteringCNVs: no visible global function definition for
'dnorm'
emnormalCNV,clusteringCNVs : <anonymous>: no visible global function
definition for 'dnorm'
groupCNVs,clusteringCNVs: no visible global function definition for
'par'
groupCNVs,clusteringCNVs: no visible global function definition for
'axis'
groupCNVs,clusteringCNVs: no visible global function definition for
'abline'
groupCNVs,clusteringCNVs: no visible global function definition for
'text'
groupCNVs,clusteringCNVs: no visible global function definition for
'hist'
plotCNVrd2,CNVrd2: no visible global function definition for 'rect'
plotCNVrd2,CNVrd2: no visible global function definition for 'text'
plotCNVrd2,CNVrd2: no visible global function definition for 'lines'
plotCNVrd2,CNVrd2: no visible global function definition for 'abline'
plotPolymorphicRegion,CNVrd2: no visible global function definition for
'ggplot'
plotPolymorphicRegion,CNVrd2: no visible global function definition for
'geom_line'
plotPolymorphicRegion,CNVrd2: no visible global function definition for
'aes'
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
'x1'
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
'x2'
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
'Quantile'
plotPolymorphicRegion,CNVrd2: no visible global function definition for
'coord_cartesian'
plotPolymorphicRegion,CNVrd2: no visible global function definition for
'theme'
plotPolymorphicRegion,CNVrd2: no visible global function definition for
'ylab'
plotPolymorphicRegion,CNVrd2: no visible global function definition for
'geom_rect'
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
'xmin'
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
'xmax'
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
'ymin'
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
'ymax'
plotPolymorphicRegion,CNVrd2: no visible global function definition for
'geom_text'
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
'x'
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
'y'
plotPolymorphicRegion,CNVrd2: no visible binding for global variable
'label'
plotPolymorphicRegion,CNVrd2: no visible global function definition for
'grid.arrange'
segmentSamples,CNVrd2 : runFunction: no visible global function
definition for 'as'
segmentSamplesUsingPopInformation,CNVrd2: no visible global function
definition for 'fitted'
segmentSamplesUsingPopInformation,CNVrd2: no visible global function
definition for 'lm'
Undefined global functions or variables:
GRanges Hsapiens Quantile ScanBamParam TabixFile abline aes
alphabetFrequency as axis chisq.test coda.samples coord_cartesian
countBam dnorm fisher.test fitted geno geom_line geom_rect geom_text
ggplot grid.arrange hist jags.model kmeans label lines lm mclapply
objectCNVrd2 p.adjust par readDNAStringSet readVcf rect text theme
unmasked update write.table x x1 x2 xmax xmin y ylab ymax ymin
Consider adding
importFrom("graphics", "abline", "axis", "hist", "lines", "par",
"rect", "text")
importFrom("methods", "as")
importFrom("stats", "chisq.test", "dnorm", "fisher.test", "fitted",
"kmeans", "lm", "p.adjust", "update")
importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calculateLDSNPandCNV 5 0.13 5.12
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/CNVrd2.Rcheck/00check.log'
for details.
CNVrd2.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/CNVrd2_1.30.0.tar.gz && rm -rf CNVrd2.buildbin-libdir && mkdir CNVrd2.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNVrd2.buildbin-libdir CNVrd2_1.30.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL CNVrd2_1.30.0.zip && rm CNVrd2_1.30.0.tar.gz CNVrd2_1.30.0.zip
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
15 2261k 15 358k 0 0 1040k 0 0:00:02 --:--:-- 0:00:02 1039k
100 2261k 100 2261k 0 0 1871k 0 0:00:01 0:00:01 --:--:-- 1873k
install for i386
* installing *source* package 'CNVrd2' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CNVrd2'
finding HTML links ... done
CNVrd2-class html
CNVrd2-package html
calculateLDSNPandCNV html
ccl3l1data html
clusteringCNVs-class html
countReadInWindow-methods html
countReadInWindow html
emnormalCNV-methods html
emnormalCNV html
fcgr3bMXL html
groupBayesianCNVs html
groupCNVs-methods html
groupCNVs html
identifyPolymorphicRegion-methods html
identifyPolymorphicRegion html
numericOrNULL-class html
plotCNVrd2-methods html
plotCNVrd2 html
plotPolymorphicRegion-methods html
plotPolymorphicRegion html
searchGroupCNVs-methods html
searchGroupCNVs html
segmentSamples-methods html
segmentSamples html
segmentSamplesUsingPopInformation-methods
html
segmentSamplesUsingPopInformation html
vectorORfactor-class html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'CNVrd2' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CNVrd2' as CNVrd2_1.30.0.zip
* DONE (CNVrd2)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'CNVrd2' successfully unpacked and MD5 sums checked
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CNVrd2.Rcheck/examples_i386/CNVrd2-Ex.timings
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CNVrd2.Rcheck/examples_x64/CNVrd2-Ex.timings
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